Role of non-covalent interactions for determining the folding rate of two-state proteins

Biophysical Chemistry

Volumn 107, Issue 3, 2004, Pages 263-272

  Gromiha, M Michael ^a   Saraboji, K ^b   Ahmad, Shandar ^c   Ponnuswamy, M N ^b   Suwa, Makiko ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF MADRAS   (India)

^c KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Amino acid properties; Correlation coefficient; Free energy approach; Hydrogen bond; Hydrophobic; Multiple regression technique; Protein folding rates

Indexed keywords

AMINO ACID; CARBON; NITROGEN; OXYGEN; PROTEIN; SULFUR;

ARTICLE; CORRELATION COEFFICIENT; ELECTRICITY; ENERGY; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR INTERACTION; MULTIPLE REGRESSION; PRIORITY JOURNAL; PROTEIN FOLDING;

EID: 1242315524     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2003.09.008     Document Type: Article

References (39)

1. Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277:1998;985-994.
2. Debe D.A., Goddard W.A. First principles prediction of protein folding rates. J. Mol. Biol. 294:1999;619-625.
3. Munoz V., Eaton W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl. Acad. Sci. USA. 96:1999;11311-11316.
4. Dinner A.R., Karplus M. The roles of stability and contact order in determining protein folding rates. Nat. Struct. Biol. 8:2001;21-22.
5. Gromiha M.M., Selvaraj S. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J. Mol. Biol. 310:2001;27-32.
6. Miller E.J., Fischer K.F., Marqusee S. Experimental evaluation of topological parameters determining protein-folding rates. Proc. Natl. Acad. Sci. USA. 99:2002;10359-10363.
7. Zhou H., Zhou Y. Folding rate prediction using total contact distance. Biophys. J. 82:2002;458-463.
8. Zhang L., Li J., Jiang Z., Zia A. Folding rate prediction on neural network model. Polymer. 44:2003;1751-1756.
9. Gromiha M.M. Importance of native-state topology for determining the folding rates of two-state proteins'. J. Chem. Inf. Comput. Sci. 43:2003;1481-1485.
10. Berman H.M., Westbrook J., Feng Z., et al. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
11. Ponnuswamy P.K., Gromiha M.M. On the conformational stability of folded proteins. J. Theor. Biol. 166:1994;63-74.
12. Eisenberg D., McLachlan A.D. Solvation energy in protein folding and binding. Nature. 319:1986;199-203.
13. S.J. Hubbard, J.M. Thornton, NACCESS, Computer program, Department of Biochemistry and Molecular Biology, University College London, 1993. Available from: http://www.wolf.bi.umist.ac.uk/unix/naccess.html.
14. Eisenberg D., Wesson M., Yamashita M. Interpretation of protein folding and binding with atomic solvation parameters. Chem. Scripta Part A. 29:1989;217-221.
15. Perutz M.F., Raidt H. Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature. 255:1975;256-259.
16. Brown L.R., De Marco A., Richarz R., Wagner G., Wuthrich K. The influence of a single salt bridge on static and dynamic features of the globular solution conformation of the basic pancreatic trypsin inhibitor. 1H and 13C nuclear-magnetic-resonance studies of the native and the transaminated inhibitor. Eur. J. Biochem. 88:1978;87-95.
17. Fersht A.R. Conformational equilibria in chymotrypsin. The energetics and importance of the salt bridge. J. Mol. Biol. 64:1972;497-509.
18. Sali D., Bycroft M., Fersht A.R. Stabilization of protein structure by interaction of alpha-helix dipole with a charged side chain. Nature. 335:1988;740-743.
19. Nicholson H., Becktel W.J., Matthews B.W. Enhanced protein thermostability from designed mutations that interact with alpha-helix dipoles. Nature. 336:1988;651-656.
20. Cornell W.D., Cieplak P., Bayly C.I., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
21. Northrup S.H., Pear M.R., Morgan J.D., McCammon J.A., Karplus M. Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements. J. Mol. Biol. 153:1981;1087-1109.
22. McDonald I.K., Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:1994;777-793.
23. Gromiha M.M., Uedaira H., An J., Selvaraj S., Prabakaran P., Sarai A. ProTherm, thermodynamic database for proteins and mutants: developments in version 3.0. Nucleic Acids Res. 30:2002;301-302.
24. Thornton J.M. Disulphide bridges in globular proteins. J. Mol. Biol. 151:1981;261-287.
25. Gromiha M.M., An J., Kono H., Oobatake M., Uedaira H., Sarai A. Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations. Protein Eng. 12:1999;549-555.
26. Gromiha M.M., An J., Kono H., Oobatake M., Uedaira H., Sarai A. Relationship between amino acid properties and protein stability: buried mutations. J. Protein Chem. 18:1999;565-578.
27. Gromiha M.M., An J., Kono H., Oobatake M., Uedaira H., Sarai A. Importance of surrounding residues for protein stability of partially buried mutations. J. Biomol. Struct. Dyn. 18:2000;281-295.
28. Gromiha M.M., An J., Kono H., Oobatake M., Uedaira H., Sarai A. Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations. Biopolymers. 64:2002;210-220.
29. Grewal P.S. Numerical Methods of Statistical Analysis. 1987;Sterling Publishers, New Delhi.
30. Vogt G., Woell S., Argos P. Protein thermal stability, hydrogen bonds, and ion pairs. J. Mol. Biol. 269:1997;631-643.
31. Gromiha M.M., Oobatake M., Sarai A. Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys. Chem. 82:1999;51-67.
32. Xiao L., Honig B. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. 289:1999;1435-1444.
33. Kumar S., Tsai C.J., Nussinov R. Factors enhancing protein thermostability. Protein Eng. 13:2000;179-191.
34. Plaxco K.W., Simons K.T., Ruczinski I., Baker D. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry. 39:2000;11177-11183.
35. Galzitskaya O.V., Garbuzynskiy S.O., Ivankov D.N., Finkelstein A.V. Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics. Proteins. 51:2003;162-166.
36. Calloni G., Taddei N., Plaxco K.W., Ramponi G., Stefani M., Chiti F. Comparison of the folding processes of distantly related proteins. Importance of hydrophobic content in folding. J. Mol. Biol. 330:2003;577-591.
37. Gong H., Isom D.G., Srinivasan R., Rose G.D. Local secondary structure content predicts folding rates for simple, two-state proteins. J. Mol. Biol. 327:(5):2003;1149-1154.
38. Makarov D.E., Plaxco K.W. The topomer search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci. 12:2003;17-26.
39. Jewett A.I., Pande V.S., Plaxco K.W. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. J. Mol. Biol. 326:2003;247-253.